Create a privkey bitcoin on your protected machine, as you want to keep your cryptocurrency safe. Please notice that the potential intruder still will be able to see your addresses, transactions and balance, though.
Now you are able to set up your electrum merchant daemon. SSL private key and a public certificate for your domain set up already. Create another file, file that contains your certificate, and the list of certificates it depends on, up to the root CA. Your certificate must be at the top of the list, and the root CA at the end. In order to display public URLs, we need to set another configuration variable, url_rewrite. Install and run Electrum-Merchant configuration program. By default it installs a simple interface, other interfaces are in preparation and will be available in future.